Variant report

Variant	rs8557
Chromosome Location	chr15:72115733-72115734
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72114514..72117570-chr15:72121768..72126233,5	K562	blood:
2	chr15:72100596..72102959-chr15:72114173..72115754,2	MCF-7	breast:
3	chr15:72114756..72117570-chr15:72121348..72123847,3	K562	blood:
4	chr15:72114725..72116485-chr15:72127394..72129983,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRAMD2-6	chr15:72114640-72115963	NONHSAT047051
2	lnc-THSD4-4	chr15:72115552-72115947	NONHSAT047052

No data

Variant related genes	Relation type
ENSG00000031544	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10851847	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11633167	0.89[CEU][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634608	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[YRI][hapmap]
rs12050794	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12439494	0.83[CEU][hapmap]
rs12898728	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12898868	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12912771	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1481862	0.81[AMR][1000 genomes]
rs16956273	0.82[CEU][hapmap]
rs16956369	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2128112	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2306576	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2415120	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2415121	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2415126	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2415128	0.89[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2723342	0.82[CEU][hapmap]
rs28650442	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28717020	0.85[AMR][1000 genomes]
rs2929508	0.86[CEU][hapmap]
rs2929509	0.85[AMR][1000 genomes]
rs2929510	0.87[AMR][1000 genomes]
rs2929511	0.88[AMR][1000 genomes]
rs2930069	0.83[AMR][1000 genomes]
rs2957724	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2957725	0.88[CEU][hapmap]
rs2957728	0.87[AMR][1000 genomes]
rs2957734	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.85[YRI][hapmap]
rs2957735	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2957737	0.88[CEU][hapmap]
rs3784310	0.94[CEU][hapmap];0.80[AMR][1000 genomes]
rs3784313	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4511483	0.84[EUR][1000 genomes]
rs4526973	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4777466	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62023343	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6494973	0.94[CEU][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6494975	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs7173626	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7175373	0.82[AMR][1000 genomes]
rs7177242	0.88[CEU][hapmap]
rs7496582	0.89[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs7497104	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8036307	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8040216	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs8178	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9302260	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs982752	0.88[CEU][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904334	chr15:71737376-72177659	Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1036938	chr15:71948106-72272855	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3331306	chr15:72049818-72427559	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv3433206	chr15:72049838-72427529	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8557	MYO9A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72108000-72118600	Weak transcription	Fetal Brain Female	brain
2	chr15:72108600-72120600	Weak transcription	Fetal Brain Male	brain
3	chr15:72110600-72118200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:72110800-72116400	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:72110800-72122800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:72111600-72116600	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
7	chr15:72111800-72116400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:72112000-72115800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:72112000-72116200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr15:72112200-72119200	ZNF genes & repeats	A549	lung
11	chr15:72112800-72118000	ZNF genes & repeats	Liver	Liver
12	chr15:72113000-72116000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:72113000-72118600	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:72113000-72118800	Weak transcription	Dnd41	blood
15	chr15:72113600-72117000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:72113800-72115800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
17	chr15:72113800-72116400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
18	chr15:72113800-72116400	ZNF genes & repeats	Left Ventricle	heart
19	chr15:72113800-72116400	ZNF genes & repeats	NH-A	brain
20	chr15:72113800-72116400	ZNF genes & repeats	NHEK	skin
21	chr15:72113800-72116600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:72113800-72116800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:72114000-72115800	Strong transcription	Fetal Intestine Large	intestine
24	chr15:72114000-72116200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:72114000-72116200	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr15:72114000-72116400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:72114000-72116400	Strong transcription	Rectal Smooth Muscle	rectum
29	chr15:72114000-72116800	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:72114000-72117000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:72114000-72117400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr15:72114200-72115800	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr15:72114200-72115800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
34	chr15:72114200-72116400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
35	chr15:72114200-72116400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
36	chr15:72114200-72116400	ZNF genes & repeats	Aorta	Aorta
37	chr15:72114200-72116400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr15:72114200-72116400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
39	chr15:72114200-72116400	ZNF genes & repeats	HMEC	breast
40	chr15:72114200-72117000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:72114200-72118600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr15:72114200-72118800	Weak transcription	Colonic Mucosa	Colon
43	chr15:72114200-72123200	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr15:72114400-72115800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr15:72114400-72116200	ZNF genes & repeats	Brain Hippocampus Middle	brain
46	chr15:72114400-72116400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:72114400-72116400	Strong transcription	Fetal Muscle Leg	muscle
48	chr15:72114400-72117000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
49	chr15:72114400-72117000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:72114400-72118000	Weak transcription	Brain Germinal Matrix	brain

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